Re: [OpenBabel-scripting] get canonical atom ordering

[Noel O'B. <bao...@gm...>]

Geoff - it might be a good idea to document these side-effects...I
wasn't aware of this one.

TJ, from O'person to another:

>>> a = pybel.readstring("smi", "CCCC(=O)")
>>> a.data.keys()
[]
>>> print a.write("can")
CCCC=O
>>> a.data.keys()
['PartialCharges', 'canonical order']
>>> a.data['canonical order']
'1 2 3 4 5'

>>> a = pybel.readstring("smi", "C(=O)CCC")
>>> a.data.keys()
[]
>>> print a.write("can")
>>> print b
CCCC=O
>>> a.data['canonical order']
'5 4 3 1 2'

If you have any further questions, please let us know.

- Noel

On 21/03/2008, Geoffrey Hutchison <ge...@ge...> wrote:
>
>  On Mar 21, 2008, at 2:05 PM, TJ O'Donnell wrote:
>
>  > Is it possible to get the canonical atom re-ordering,
>  > say as an int vector, after conversion to canonical smiles?
>
>
> As a matter of fact, yes. The current SVN trunk has this feature --
>  after conversion to canonical SMILES, the ordering is available as an
>  OBPairData called "Canonical Atom Order"
>
>  For a C++ example, of this, check out tools/obfragment.cpp.
>
>  This should be accessible from Python directly, although I defer to
>  Noel on the Pybel syntax for this.
>
>  Cheers,
>  -Geoff
>
>
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